jalview

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JAL-3225 tasks to create extra desired settings for eclipse

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    /utils/eclipse/org.eclipse.jdt.groovy.core.prefs
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    /utils/eclipse/org.eclipse.jdt.ui.prefs
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into Jalview-JS/develop

Merge branch 'documentation/Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

Merge branch 'documentation/Release_2_11_1_Branch' into develop

JAL-3407 basic doc for releasing jalview - will be embellished as we go

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    /doc/releaseprocess.md
Merge branch 'documentation/Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

JAL-3407 updated release date to 2nd April, and first draft of release notes

Merge branch 'develop' into Jalview-JS/develop

JAL-1889 better (?) wait for Conservation thread

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    /test/jalview/gui/AlignViewportTest.java
JAL-3248 quick fix to not remove doc/building.html with a gradle clean

JAL-3210 JAL-3130 merge changes to JSON processing

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    /src/jalview/ext/paradise/Annotate3D.java
Merge branch 'develop' into Jalview-JS/develop

Merge branch 'documentation/Release_2_11_1_Branch' into develop

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

JAL-3393 Don't need PDF file using Illustrator. Replaced with SVG using Inkscape

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    /utils/install4j/jalview_dmg_background_layers.pdf
JAL-3407 2.11.1.0 release date bump - maybe tomorrow - maybe the next day !

JAL-3407 JAL-3130 back out java 9+ syntax that breaks java 8 builds

JAL-3210 merged from develop: build.gradle and gradle.properties

JAL-3210 debug logging commented out

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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3210 test updated for changed signature of SequenceI.getDBRefs()

Merge branch 'develop' into Jalview-JS/develop

Conflicts:

.gitignore

build.gradle

gradle.properties

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/JvSwingUtils.java

src/jalview/util/MessageManager.java

test/jalview/gui/AlignmentPanelTest.java

test/jalview/gui/JvSwingUtilsTest.java

test/jalview/gui/PopupMenuTest.java

utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/FeatureSettings.java
  1. … 19 more files in changeset.
JAL-3225 updated essential files for eclipse project if buildship fails

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    /utils/eclipse/eclipse_startup_files.zip
JAL-3225 updated essential files for eclipse project if buildship fails

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    /utils/eclipse/eclipse_startup_files.zip
JAL-3562 paranoid print out of tested values during wait suspect a platform issue making result different

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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3225 Also look for local.properties in file named ../${projectDir}_local.properties. This allows multiple instances of the same project in Eclipse by changing the eclipse_project_name propert (and other local properties)

JAL-3225 This one file needed for project if git clean -dfx run

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    /.settings/org.eclipse.buildship.core.prefs
JAL-3225 This one file needed for project if git clean -dfx run

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    /.settings/org.eclipse.buildship.core.prefs
JAL-3225 fix comparing Eclispe IDE j2s plugin and this branch j2s plugin

JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.core.jalview.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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    /utils/eclipse/org.eclipse.jdt.core.jalview.prefs
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    /.settings/org.eclipse.buildship.core.prefs
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    /.settings/org.eclipse.jdt.core.jalview.prefs
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    /.settings/org.eclipse.jdt.groovy.core.prefs
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    /.settings/org.eclipse.jdt.ui.prefs
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    /utils/eclipse/org.eclipse.jdt.core.jalview.prefs